new lift pump installed truck starts hard now

[SServey]

I had a problem with the engine shaking and losing power on a long hill in Yakima. Cummins checked everything and adjusted the waste gate and timing. Then decided the lift pump was bad. My home to Seattle was slow and it shook and tried to cut out once on a long hill and the engine was real sluggish. The next day I pulled the tank and checked the screen (clean). I accidentally crossed the fuel lines at the tank and I must have pushed that priming button about 500 times. In the process of trying to bleed the air out after switching the fuel lines the right way I noticed fuel leaking out the water sensor (the handle was broken off) so I replaced that. Now the engine is OK but it still feels pretty under-powered. My problem now is that it is real hard to start (like when you have air in the lines)..If I push the prime button afew times (I can hear the fuel come in to the pump,) before starting it, it makes it alot easier to start. Once it starts after a few seconds it smooths out but initially there is enough smoke to drive my wife out of the front yard. After driving about a half mile the smoke goes away. I've checked and triple checked all the lines I have loosened. I took off the rubber hose in front of the pump to put a screw-on hose clamp on and was surprised to find no fuel in that line. This problem of ruff/hard start occurs only after setting around a half hour or more. Are there any other checks I can make to diagnose this problem? This is a 94/12 valve with 189k